Finding main transcripts from SOAPdenovo-trans results

[Melissa]

Hi guys, do you know how I can get the main/best/longest transcripts for each locus in my SOAPdenovo-trans assemblies? I'm not interested in the alternative splicing isoforms. When I used the locusMaxOutput option -t 0, it gave me all the transcripts per locus. When I used locusMaxOutput option -t 1, it gave me maximum two transcripts per locus (locus_x_0 and locus_x_1). I'm currently using the first transcript from each locus (locus_x_0), however, I'm not sure if this is the main transcript.

Thanks for your help in advance!